- ChimeraX-users - RBVI Mailing Lists

ISOLDE refine.eff and phenix.refine
by Shawn Rumrill 13 Mar '25

13 Mar '25

Dear ChimeraX Community, Not strictly ChimeraX related, but probably interesting to some and I've seen some feedback for ISOLDE here... I am using ISOLDE to rebuild a mid-resolution protein/NA model (still adjusting to using ISOLDE, but really powerful tool). I want to refine using phenix.refine, but I am running into a problem with the refine.eff file. The error from the terminal output is below. I've gathered that this is due to a change in parameter terminology from Phenix 1.20 to 1.21. My question is, is there some way to write the refine.eff file with the required information? I would hate to have to manually edit the .eff output file each time I want to run a new refinement in Phenix. Thanks, Shawn Error: Processing files: ------------------------------------------------------------------------------- Found phil, refine.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ refine.eff Unrecognized PHIL parameters: ----------------------------- refinement.input.pdb.file_name (file "refine.eff", line 6) refinement.input.xray_data.file_name (file "refine.eff", line 9) refinement.input.xray_data.labels (file "refine.eff", line 10) refinement.input.xray_data.high_resolution (file "refine.eff", line 11) refinement.input.xray_data.low_resolution (file "refine.eff", line 12) refinement.input.xray_data.r_free_flags.file_name (file "refine.eff", line 14) refinement.input.xray_data.r_free_flags.label (file "refine.eff", line 15) refinement.input.xray_data.r_free_flags.test_flag_value (file "refine.eff", line 16) Sorry: Some PHIL parameters are not recognized by phenix.refine. Please run this program with the --show-defaults option to see what parameters are available. PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")

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Re: Inquiry to docking protein onto lipid bilayer
by You, Youngki 12 Mar '25

12 Mar '25

Hello Tommy, You can use this server (PPM in OPM site), https://opm.phar.umich.edu/ppm_server3_cgopm , to determine the orientation and depth of your protein in the membranes. After that, you can use the model from PPM in CHARMM-GUI. Best, Youngki ________________________________PNNL__ Youngki You, PhD Post Doctorate RA, Biochemical Mechanisms Structure, Function & Design Biological Sciences Division Pacific Northwest National Laboratory Tel: +1 (509) 371-6660

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Inquiry to docking protein onto lipid bilayer
by Tommy Tong 12 Mar '25

12 Mar '25

Dear ChimeraX experts, Good afternoon. My name is Tommy from San Diego Biomed. I am a beginner to ChimeraX version 1.9. May I ask if it is possible to use ChimeraX to dock a membrane protein into a lipid bilayer? I obtained Phosphotidylcholine bilayer (POPC) structure from CHARMM-GUI webpage https://charmm-gui.org/?doc=archive&lib=lipid_pure, and was wondering if it is possible to “place” a protein into this POPC structure in ChimeraX. Your help and advice on this is greatly appreciated. Thank you. Sincerely, Tommy

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Obtain individual RMSD values
by javisanchezdelrio＠gmail.com 12 Mar '25

12 Mar '25

Hello, I have an issue when applying matchmaker command in ChimeraX. When I execute the command: matchmaker #1 to #2 showAlignment true I obtain the alignment with the bars in the upper layer showing the individual RMSD of each residue. But the results yields the overall RMSD of the alignment (i.e. RMSD between 108 pruned atoms). Is there any way to obtain those individual RMSDs of the alignment as a file or have them printed in the log for post-processing? Thank you in advance

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Dividing a huge model (& map) into smaller chunks
by Alejandro Buschiazzo 12 Mar '25

12 Mar '25

Dear chimeraX developers/users Using version 1.9, I am trying to divide a very big mmcif model (230K + nonH atoms; >130 chains) and corresponding mrc map, into a number of smaller mmcif files (and corresponding cropped maps, covering just those parts). What I’ve tried so far unsuccessfully: I can create dummy atoms with build start atom, at desired x,y,z points, so that I can then use select zone to select a radius and keep parts near each dummy atom. Yet, that is suboptimal: I would largely prefer to keep (build) boxes, and not spheres, ensuring complete recovery and no blind spots. So that each box slightly overlaps with the neighboring one, and systematically covers the whole original map volume. 1. How can I generate a script that will do this "systematic windowing” screening, making boxes of a defined side-length at each step, and keeping the model within? 2. How should I then crop the original map, so that it covers each box (with a small padding on the borders)? 3. How should I stitch back the models, so that I don’t loose any atomic coordinates information? (of course that stitching will be done after I do some refinement work on each boxed model vs map) So sorry for the many questions! I’ve been trying hard to find this kind of strategy, and just can’t seem to succeed…. Thank you very much in advance Alejandro -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 ext. 120 Fax: +598 25224185 https://pasteur.uy/en/laboratories/molecular-and-structural-microbiology/

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General ?s - Foldseek (Sequence Plot) and Similar Structures Table
by Emir MALOVIC 11 Mar '25

11 Mar '25

Hello, Quick question: When I load the sequence plot, I receive 2 sequence images separated by a very large black space. When I save the image as a PNG, the black space between the sequence images is retained. Basically, the image is mostly black space. Is there a way to change that or is this a bug? Am I able to somehow copy the Similar Structures table or export it into Excel? A copy/paste function would be ideal and quick. I am using the Chimera 1.10 dev. Please let me know at your earliest convenience! Thank you, Emir

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Suggestion for improvement
by James Raymond 11 Mar '25

11 Mar '25

I love ChimeraX and use it often for my work, e.g. this one <https://www.pnas.org/doi/10.1073/pnas.2421910122>. When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas

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What is the .exe file for ChimeraX Toolbox?
by m.i.bashir＠bham.ac.uk 11 Mar '25

11 Mar '25

Hi all, First time posting here. I'm looking to find the name and location of the file/folder that manages the ChimeraX in-app browser. The way I launch the browser is to go to 'tools' in the top bar, then press 'more tools', and then it brings up the ChimeraX Toolshed Where is the .exe file that controls this in app browser? I am attempting to find the .exe file and black list it, so we can use ChimeraX for an exam Thanks,

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SASA in MDS
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I am sorry; I did not state the subject of my previous email. I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

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(no subject)
by Gabriel López Velázquez 10 Mar '25

10 Mar '25

Dear Elaine, I would ask for help. How can I calculate SASA as a function of time from the MD simulations in Chimerax? What archives need to perform it? Thanks in advance! Gabriel.

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Inquiry About Favorable Contacts and Display Methods in ChimeraX
by 田畑　健士郎 07 Mar '25

07 Mar '25

Subject: Inquiry About Favorable Contacts and Display Methods in ChimeraX Dear ChimeraX Developers, My name is Kenshiro Tabata. I hope this email finds you well. I am currently using ChimeraX to analyze the effects of point mutations on protein structure, particularly in cases where a larger side chain (e.g., methionine) is replaced by a smaller one (e.g., valine). In such cases, I expect that interactions with the opposing amino acids may be reduced due to the decreased side-chain volume. To investigate this, I would like to ask for your guidance regarding the interpretation and visualization of favorable contacts. ________________________________ 1) Understanding Favorable Contacts I understand that the contacts command identifies all types of interactions, whereas the clashes command detects only unfavorable interactions. Based on this, I interpreted the positive VDW overlap as indicating unfavorable (repulsive) interactions, while an overlap between 0 and -0.4 represents favorable (attractive) interactions. Could you confirm if this understanding is correct? ________________________________ 2) Best Approach for Displaying Only Favorable Contacts To analyze how the mutation affects interactions, I would like to display only favorable contacts. Below is the approach I have considered: Proposed Approach 1. Retrieve all interactions (favorable, neutral, and unfavorable) using the contacts command contacts overlapCutoff -0.4 saveFile all_contacts.txt 2. Retrieve only neutral and unfavorable interactions contacts overlapCutoff 0 saveFile non_favorable_contacts.txt 3. Compute the difference between these two sets using Python, extract only favorable contacts, and format them into a ChimeraX pseudobond file # File paths all_contacts_path = "all_contacts.txt" non_favorable_contacts_path = "non_favorable_contacts.txt" favorable_contacts_path = "favorable_contacts.pb" # Read files with open(all_contacts_path, "r") as f: all_contacts = set(f.readlines()) with open(non_favorable_contacts_path, "r") as f: non_favorable_contacts = set(f.readlines()) # Extract favorable contacts favorable_contacts = all_contacts - non_favorable_contacts # Convert to ChimeraX pseudobond file format with open(favorable_contacts_path, "w") as f: f.write("; Pseudobond file for favorable contacts\n") f.write("; radius = 0.1\n; color = green\n; dashes = 6\n") for line in favorable_contacts: parts = line.strip().split() if len(parts) >= 4: atom1 = f"/{parts[0]}:{parts[1]}@{parts[2]}" atom2 = f"/{parts[3]}:{parts[4]}@{parts[5]}" f.write(f"{atom1} {atom2}\n") 4. Load the extracted favorable contacts into ChimeraX for visualization open favorable_contacts.pb Would this be an appropriate approach? Alternatively, is there a simpler or more precise way to achieve this in ChimeraX? I appreciate your time and assistance, and I look forward to your advice. Best regards, Kenshiro Tabata

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AI in ChimeraX
by Elaine Meng 07 Mar '25

07 Mar '25

On Mar 7, 2025, at 6:01 AM, Veach, Kevin G. <kevin.veach(a)uky.edu> wrote: > > Hi Elaine: > Does Chimera-X use Artificial Intelligence or Large Language Learning Models? > Thank you, > > Kevin > Kevin Veach, Computer Support Specialist II > University of Kentucky, Animal & Food Sciences Dept. Hi Kevin, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for general questions about ChimeraX -- I'm not the top expert on all parts of ChimeraX, so you may get better answers from other developers or our user community. Regarding your question, my understanding is that ChimeraX itself does not use these kinds of calculations, but it has tools that interface to web services or other calculations (run outside of ChimeraX) that do use them. The ones that I can think of are AlphaFold/ColabFold and ESMFold: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html#predict> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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Creating movie in ChimeraX from YASARA simulation
by ibogdanov 07 Mar '25

07 Mar '25

Hi ! I have the following question - How can I create a movie, when I cannot use the YASARA.sce file from which I converted/extracted xtc.file(the trajectories) when I have all the snapshots(pdb and sim.files) created as separate files during the performed simulation in YASARA...I've uploaded for example the first pdb file of the series and the xtc.file but isn't the saved xtc.file(trajectories) of the whole simulation(for all the structures)? How would you suggest me to solve this problem, if ChimeraX doesn't support sce.files ? Thank you in advance! Kind Regards, Ivan Bogdanov

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Problem installing on OSX
by Thom Hughes 06 Mar '25

06 Mar '25

I apologize for the dumb question, but here it is. I want to install the isolde extension. When I go to more tools, isolde, and click the install button a .whl file downloads correctly. But then nothing happens. I’m running OSX 15.3.1. thanks in advance for any pointers!

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Unable to open the file after downloading ChimeraX
by Guo-Ping Zhou 05 Mar '25

05 Mar '25

Dear Sir/Madam, After downloading ChimeraX, I automatically get the attached .png in the application as a microsoft word file. However, I can't open the Quick Access Toolbar. Could you please tell me how to make it work? Thanks! Guo-Ping Zhou, Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804

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(no subject)
by FRANGIE Christian 05 Mar '25

05 Mar '25

Dear UCSF ChimeraX Support Team, My name is Christian frangieh, I am currently using Chimera X to visualize my AlphaFold simulations, and I want to check when i introduce a mutation and change one residue (amino acid), whether there is a change in the surface accessibility of the residue. Currenlty i am checking this visually by checking whether the residue is exposed to the surface or hidden. Nevertheless, i would like to know how can i do this with a command or by some form of calculation or structural analysis. Can you please help me with this matter? Warm Regards, Christian

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Can not find Structure Minimization in ChimeraX menu
by N.B. Nugroho 04 Mar '25

04 Mar '25

Dear ChimeraX developers I a little bit confuse to find the Structure Minimization menu in ChimeraX. In Chimera 1.16 it located in menu Tools>Structure Editing>Minimize Structure. Could you please guide me for this little problem. Best regards Nuki B Nugroho

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(no subject)
by junjie han 02 Mar '25

02 Mar '25

Hi, I hope you are doing well. May I ask two questions? First one: Why does the connection part between the side chain and backbone, which is circled in a dashed line in ChimeraX, look so abnormal? How can I make it display normally? [cid:437c0c59-2e31-4251-ac9c-eff3f64af0dd] Second one: Is it possible to show the border only for a specific region of protein without hiding other regions? Thanks, Junjie

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define integer attributes for multiple individual pseudobonds
by hannes.ludewig＠googlemail.com 28 Feb '25

28 Feb '25

Dear developers, I am trying to color pseudobonds by an individual (per-bond) attribute value (integer). I seem to be unable to use .pb files to create individual pseudobonds. And when I am using the pbond command several times providing an individual name for each pseudobond thus creating individual models (#1.1, #1.2, etc) I am unable to assign an attribute and color all pseudobonds according to the corresponding attribute value. What I want to create is similar to the alphafold contacts colored by PAE. Only that the values I am providing aren't PAE and I would like to determine the residue pairs that form each pseudobond. I apologize in case I am overlooking something obvious, but your help and/or clarification would be very much appreciated. Thank you. Best wishes, Hannes

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Disulphide bridges in ISOLDE
by Guillaume Gaullier 28 Feb '25

28 Feb '25

Hello ISOLDE users and Tristan, Is there a distance threshold at which ISOLDE won't let me close a disulphide bridge? I am puzzled, because it seems I can close a disulphide between two Cys about 10 residues apart in sequence and quite far from each other in space. In fact much further apart than a bond length, so the resulting bond looks ridiculously stretched. But it is quickly fixed when running a local simulation, even if it needs to pull the backbone out of density to achieve a reasonable S-S bond length. In the same model, I have two other Cys that follow each other in sequence. When loading the AlphaFold prediction, the two S atoms are close enough (for some reason) that ISOLDE offers to make the disulphide, so I say yes. Later on, wanting to test both options to assess which one is best supported by the map, I can break this disulphide, but once I do there is no way to close it again. In this case, the two S atoms settle about 3.4 Å apart when removing the bond, which is longer than an ideal disulphide, but much shorter than the distance over which ISOLDE still allowed me to form a disulphide in the first case. The documentation doesn't say anything about disulphides (or somehow I missed it). In fact, there seems to be no command to operate on disulphides? Using the menu item does not write anything to the Log, so if there is a command I cannot find what it is and what options it might accept. If someone can help with this, I would appreciate it! Thank you, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Lägerhyddsvägen 1 752 37 Uppsala Sweden När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Assistance Required: Extracting List of Interacting Residues within 4 Å in UCSF Chimera
by Rashmi Aggarwal 27 Feb '25

27 Feb '25

Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: 1. *Select residues* in one molecule that are within 4 Å of the other molecule. 2. *Generate and export a list* of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi

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Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 27 Feb '25

27 Feb '25

Dear colleagues I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help? [cid:image001.png@01D9D154.CE3D4440] Best, - - - - - - - - - - - - - - - - - Miao Zhang Ph.D. Associate Professor Chapman University School of Pharmacy 9401 Jeronimo Rd, Suite 297W Irvine, CA 92618 Phone: 714-516-5478 http://www.chapman.edu/our-faculty/miao-zhang

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Cannot click popup windows in ChimeraX WSL installation
by Jobichen 26 Feb '25

26 Feb '25

Hi All,I am unable to click on any popup windows in my chimeraX installation. For eg: colour menu, once popped up, unable to click on any options.Ubuntu 22.04.5 LTS installed under WSL in Dell laptop. ChimeraX ver 1.9Error messages:NOTE: available bundle cache has not been initialized yetmalloc(): unsorted double linked list corruptedAborted (core dumped) Any suggestions.Thank you.Jobi

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Rotation using left mouse button
by y.v.hazendonk＠nki.nl 26 Feb '25

26 Feb '25

Hello, In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn't suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance. With kind regards, Yorick van Hazendonk

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Communicate between multiple ChimeraX instances
by Roden Deng Luo 25 Feb '25

25 Feb '25

Hi, I wonder if there is a way to synchronize two or more ChimeraX instances/sessions. For example, sync the camera. The meeting command ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/meeting.html) a great command I just got to know, is very close to what I am looking for. Only I will have different data in different instances, and toggles to enable and disable what features to be synced. If it is not currently implemented, how should I approach it as a developer? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Measure angle between domains in chimeraX
by junjie han 24 Feb '25

24 Feb '25

Hi Elaine, I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1: [cid:ee5ac0af-a9be-4e98-bb7c-e555c8f183c2] How to calculate these angles (54°, 38°)？ Example 2: [cid:24512415-5303-4be2-8f61-a4fd6acdc0ee] How to calculate this angle (75°) ? Example 3: [cid:f3ed355d-a961-4647-8a3c-b39ab3875cb8] How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel. Thank you in advance for your any suggestions. Very appreciated, Junjie

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Trouble Morphing 2 Proteins
by Andrew Mejia Garnica 24 Feb '25

24 Feb '25

Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew

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Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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Freelance vs. Agency – Best Choice for Native App Developers Houston?
by hooria.khan＠algoace.com 23 Feb '25

23 Feb '25

I’m trying to decide whether I should hire a freelance developer or work with an agency for my native app development needs. Freelancers can be more affordable, but agencies offer structured project management. Are there any experienced <a href="https://algoace.com/houston-app-development/">Native App Developers Houston</a> who work independently and provide top-notch services? On the other hand, if you’ve worked with an agency, was the cost worth it? Any recommendations based on your experience?

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Update chain description from fasta file
by Paul Sauer 23 Feb '25

23 Feb '25

Hi, I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed? Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known. I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well. Thank you to the Chimerax team & contributors for creating such a great program, Paul

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Dear ChimeraX users!
by amiraziznezhad＠gmail.com 23 Feb '25

23 Feb '25

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files msuic). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.myeasymusic.ir/ Many thanks in advance! Cheers Enrico

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RspProp
by Robert Stanley 23 Feb '25

23 Feb '25

Hello - I was wondering what I have to do to install the RspProp tool? It doesn't appear in my utilities menu or the structure analysis one. I have version 1.9 (2024-12-11). I very much appreciate this program and use it in my Biochem and Biophysical Chemistry courses to expose the students to it ASAP. Thanks, Bob Stanley Robert J. Stanley, Ph.D. Professor of Chemistry 1901 N. 13th St., 250B Beury Hall Temple University Philadelphia, PA 19122 (215) 204-2027 https://www.cst.temple.edu/~rstanley/

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Contribute to ChiemraX Recipe
by NG, Cheukhei Jackie [Student] 22 Feb '25

22 Feb '25

Dear ChimeraX Development Team, I am Jackie NG from a cryoEM group in the Hong Kong Polytechnic University interested in molecular visualization and analysis. I am writing to express my interest in contributing scripts to the ChimeraX library, specifically for inclusion in the ChimeraX Recipes. Sharing my scripts could benefit the community and enhance the utility of ChimeraX for various applications. The scripts are mainly quality-of-life improvements on copying selected parts of models, producing map-quality representations, organizing ligand chains, and many more. Please let me know if there is a process for submitting these scripts and any specific guidelines I should follow. I am eager to collaborate and contribute to the ongoing development of ChimeraX. Thank you for considering my contribution. I look forward to your response. Best regards, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature-v2.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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Aligning fasta sequence with the sequence of pdb model in chimeraX
by Rayees Mattoo 21 Feb '25

21 Feb '25

Hi, I was wondering if there is a way in chimeraX to align fasta sequence with sequence from the loaded pdb model. Just wanted to be sure that the residue numbering matches the original Uniprot sequence. Any other suggestions that can do the job quickly are welcome. Best, Rayees

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(no subject)
by FRANGIE Christian 21 Feb '25

21 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You

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save clipped volume
by Yanhe Zhao 20 Feb '25

20 Feb '25

Greeting there ChimeraX developer and community, I have "clip" used on my map and currently want to save the clipped one as a new mrc file, what is the best way to do this? I checked the "save Map" command and found the region option, but I don't think it is the right option if I have my clip plan tilt. Thanks a lot for any input. Thanks and cheers, Yanhe

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Help Needed with Building Capsid for ssRNA Homolog
by Bruno Hay Mele 20 Feb '25

20 Feb '25

Hi everyone, I am trying to build the capsid for a homolog of Chaetoceros socialis forma radians RNA virus 1 (PDB: 8b38). My approach was to work by homology, transferring the assembly/symmetry information from the PDB entry to my model, which I built by assembling homologs of the three subunits of 8b38. Unfortunately, this has not been as straightforward as I hoped. Ibm a complete newbie in this area, and my attempts to copy the relevant parts of the assembly information or use the ChimeraX bsymb tool have led nowhere. Could someone please point me to the right solution? Ibd really appreciate both: A practical solution: How to correctly transfer the symmetry information and generate the full capsid assembly in ChimeraX. Some references or explanations: Resources that explain why the solution works this way, so I can understand the underlying principles. Any help or pointers would be very much appreciated. Thank you very much for your time and assistance. Cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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ChimeraX Model Joining
by Nieder, Claire 20 Feb '25

20 Feb '25

Hey there, I am a grad student at UConn trying to covalently link two PDB models by inserting a GFP into the third intracellular loop of 5HT4. If you have any advice, I would really appreciate it. Thanks, Claire Nieder Kienzler Lab UConn Chemistry

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(no subject)
by FRANGIE Christian 20 Feb '25

20 Feb '25

Dear UCSF ChimeraX Support Team, My name is christian frangieh, I am currently using chimera x and i want to check the interacting residues that form the interface between 1 chain with 2 other different chains. for example my model has 3 chains (chain A,B,C) i want to have a list of the resideus of chain A and B that are interacting with chain C Can you please help me with this? Thank You christian

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Re: [Chimera-users] script for clashes
by Eric Pettersen 18 Feb '25

18 Feb '25

Hi Valerio, Well, one of the main motivations for using ChimeraX is that running commands actually return results instead of nothing. So the 'clashes' command returns a dictionary of the clashes, as described here: https://github.com/RBVI/ChimeraX/blob/1bae62d955f4b9d6d05a31541af0372f11d36… . Therefore you do not need all that extra code that Chimera needs to try to determine if there were any clashes. Instead it's just: clashes = run(session, "clashes") if clashes: # code for existing clashes else: # code for no clashes Now, reasonable structures should have at most a few clashes, and usually zero, not many thousands like your structures seem to have. I suggest opening one of the structures interactively in ChimeraX, run the "clashes" commands and look to see why there so many clashes. --Eric > On Feb 17, 2025, at 3:03 AM, chiarini(a)takisbiotech.it wrote: > > Dear Prof Pettersen, > > Thank you so much for your advice. So far I managed to operate in chimeraX and now I can see the outputs of my script. righ now I'm running the following: > > > # -*- coding: utf-8 -*- > > import os > from chimerax.core.commands import run > > # Funzione principale che accetta la sessione > def process_pdb_files(session): > # Specifica la cartella con i file PDB > folder_path = "C:/Users/utente/Desktop" # Modifica il percorso della cartella > > # Stringa da cercare nei file > search_string = "A3a" > > # Lista dei file PDB nella cartella > file_names = [fn for fn in os.listdir(folder_path) if fn.endswith(".pdb")] > > # Stampa dei file trovati nella cartella per debugging > print("File trovati nella cartella:", file_names) > > # Loop su ogni file che contiene 'search_string' nel nome > for pdb_file in file_names: > if search_string in pdb_file: > pdb_path = os.path.join(folder_path, pdb_file) > > # Apre il file PDB > print(f"Apertura del file {pdb_file}...") > run(session, f"open {pdb_path}") > > # Calcola i clash (comando corretto per ChimeraX) > run(session, "clashes") > > # Verifica se ci sono clash > clashes_found = False > for m in session.models: > if getattr(m, 'category', None) == "contacts": > clashes_found = len(m.pseudoBonds) > 0 > if clashes_found: > break > > # Se ci sono clash, elimina il file > if clashes_found: > os.remove(pdb_path) > print(f"Clash trovati, il file {pdb_file} è stato eliminato.") > else: > print(f"Nessun clash trovato per {pdb_file}.") > > # Chiude il modello dopo averlo processato > run(session, "close all") > > # Questa parte assicura che la funzione venga chiamata correttamente > def main(session): > process_pdb_files(session) > > # Quando esegui lo script in ChimeraX, la sessione viene passata automaticamente > main(session) > > AND I GOT THE FOLLOWING OUTPUT: > > runscript C:/Users/utente/Desktop/chimera_script2.pyFile trovati nella cartella: ['A3a_structure_1.pdb', 'A3a_structure_2.pdb', 'A3a_structure_3.pdb', 'A3a_structure_4.pdb', 'A3a_structure_5.pdb'] > Apertura del file A3a_structure_1.pdb... > open C:/Users/utente/Desktop\A3a_structure_1.pdb > Chain information for A3a_structure_1.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes84336 clashes > Nessun clash trovato per A3a_structure_1.pdb. > close allApertura del file A3a_structure_2.pdb... > open C:/Users/utente/Desktop\A3a_structure_2.pdb > Chain information for A3a_structure_2.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes655434 clashes > Nessun clash trovato per A3a_structure_2.pdb. > close allApertura del file A3a_structure_3.pdb... > open C:/Users/utente/Desktop\A3a_structure_3.pdb > Chain information for A3a_structure_3.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes626886 clashes > Nessun clash trovato per A3a_structure_3.pdb. > close allApertura del file A3a_structure_4.pdb... > open C:/Users/utente/Desktop\A3a_structure_4.pdb > Chain information for A3a_structure_4.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes482406 clashes > Nessun clash trovato per A3a_structure_4.pdb. > close allApertura del file A3a_structure_5.pdb... > open C:/Users/utente/Desktop\A3a_structure_5.pdb > Chain information for A3a_structure_5.pdb #1 > Chain Description > 0 2 4 6 8 C E G I K M O Q S U W Y a c e g i k m o q s u w y No description available > 1 3 5 7 9 B D F H J L N P R T V X Z b d f h j l n p r t v x z No description available > A No description available > clashes315894 clashes > Nessun clash trovato per A3a_structure_5.pdb. > close all > > > WHAT ELUDES ME IS THAT FOR EACH STRUCTURE CHIMERA FINDS LOT OF CLASHES BUT THEN RETURNS THE STATMENT "NO CLASH FOUND FOR STRUCTURE X". Why is that? I know these structures have lots of overlapping atoms and it also seems that chimera counts the class "clashes". But maybe it also includes contacts? > I would like to count only steric clashes and atoms superposition which makes the structure impossible. > Thanks in advance for your help. > > Best regards, > > Valerio Chiarini > > Il 2025-02-12 21:06 Eric Pettersen via Chimera-users ha scritto: >> Hi Valerio, >> I should preface things by saying that this script would be >> considerably easier to write in ChimeraX, because in ChimeraX the >> "runCommand" equivalent actually returns results from the command >> instead of nothing. So in ChimeraX you can directly determine if the >> clash-finding command actually found any clashes. >> So clearly the body of your 'if' statement never executed since it >> includes illegal statements that would have produced errors if the >> body of the 'if' statement had been executed, whereas you got no >> output. So the first thing is put "print file_names" right after the >> line that sets files_names and see if any of the file names contain >> your search string ("xxx"). If none of them do, then you need to >> figure out why: is folder_path wrong?; is search_string wrong?; do the >> files not end in .pdb?; etc. >> In addition, I can see some problems even if the 'if' statement body >> had executed. You don't close the models at the end, so they will >> build up and "findclash" will find more and more clashes. Your actual >> findclash command needs to be "findclash #0 test self". There is no >> "chimera.clashClashList". Probably the simplest way to determine if >> clashes were found is checking if the clashes pseudobond group has any >> pseudobonds in it. You can do that with: >> for m in chimera.openModels.list(hidden=True): >> if getattr(m, 'category', None) == "contacts": >> clashes_found = len(m.pseudoBonds) > 0 >> break >> --Eric >> Eric Pettersen >> UCSF Computer Graphics Lab >>> On Feb 12, 2025, at 2:23 AM, valerio chiarini via Chimera-users >>> <chimera-users(a)cgl.ucsf.edu> wrote: >>> Dear Responsible, >>> I am working on a script that should iterate through several >>> structures, check the structures for clashes among all atoms, and >>> eliminate the pdb in any clashes are found. >>> Here is what I have worked out so far: >>> # -*- coding: utf-8 -*- >>> import os >>> from chimera import runCommand as rc >>> from chimera import replyobj >>> import chimera >>> # Specify folder >>> folder_path = "/gporq3/store_0/usr/chiarini/chroma/chroma/" >>> # String to be found >>> search_string = "xxx" >>> # List of files in the folder >>> file_names = [fn for fn in os.listdir(folder_path) if >>> fn.endswith(".pdb")] >>> print("File trovati nella cartella:" + str(file_names)) >>> # Loop on every file containing 'search_string' in the name >>> for pdb_file in file_names: >>> if search_string in pdb_file: >>> pdb_path = os.path.join(folder_path, pdb_file) >>> # Open the PDB >>> rc("open {}".format(pdb_path)) >>> # Calculates clashes >>> rc("findclash") >>> rc("wait") >>> # Verify if any clashes are found >>> clashes = chimera.clashClashList() >>> if clashes: >>> # If clashes are found eliminates the file >>> os.remove(pdb_path) >>> print("Clash trovati, il file {} è stato >>> eliminato.".format(pdb_file)) >>> else: >>> # If no clash, exit normally >>> print("Nessun clash trovato per {}.".format(pdb_file)) >>> But no analisys is done at all. I have been searching through the >>> script page (https://www.rbvi.ucsf.edu/trac/chimera/wiki/Scripts) in >>> order to found some clue on this function but so far I have found >>> none. >>> Could you help me on this issue? >>> Thank you in advance >>> Valerio Chiarini _______________________________________________ >>> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu >>> Archives: >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ >> _______________________________________________ >> Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/ > > -- > Dr. Valerio Chiarini > > _Senior Scientist_ > > Proteins & Monoclona Antibodies Department – Takis Biotech > > c/o Tecnopolo > > Via di Castel Romano, 100 > > 00128 Rome, Italy > > Tel.: +39 06-50576077 > > Fax: +39 06-50576710 > > Email: chiarini(a)takisbiotech.it > > Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.takisbiotech.it&d=D… > > D_.lgs. 196/03_ > > _Le informazioni contenute in questa comunicazione e gli eventuali > documenti allegati hanno carattere confidenziale, sono tutelate dal segreto > professionale e sono ad uso esclusivo del destinatario. Nel caso questa > comunicazione Vi sia pervenuta per errore, Vi informiamo che la sua > diffusione e riproduzione è contraria alla legge e preghiamo di darci > prontamente avviso e di cancellare quanto ricevuto. __Grazie._ > > _This e-mail message and any files transmitted with it are subject to > attorney-client privilege and contain confidential information intended > only for the person(s) to whom it is addressed. If you are not the intended > recipient, you are hereby notified that any use or distribution of this > e-mail is strictly prohibited: please notify the sender and delete the > original message. __Thank you._ >

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Bundle development for chimeraX - svg onClick event to run command from QWebEngineView
by Lou Holland 18 Feb '25

18 Feb '25

Hello, Apologies if this is the wrong email address to contact about this. I am currently working on a privateer bundle for carbohydrate validation in chimeraX. At present, I have it so that the privateer tool will display SNFGs of glycans present in the structure using svgs displayed in a QWebEngineView(). I would like, if possible, on clicking elements of the svg to run a chimeraX command (view /chainID:resID) to centre the view window on the residue in question. At present, I can implement an onClick event to display the command that should be run, but haven't managed to figure out how to just run the command from within that QWebEngineView. Is there a mechanism already in place for doing something like this that I could take advantage of? I'd considered using the "log html" to display the svgs in the log instead of the WebEngineView() so that I could take advantage of the href="cxcmd" functionality, but the svgs are long, with semicolons and new-line characters which interfere with this. Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

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Assistance with ChimeraX Syntax for SPRITE Hands-On Module
by Zeenat Bashir 18 Feb '25

18 Feb '25

Dear ChimeraX Developers, I hope this email finds you well! I am currently developing a hands-on module for my students on visualizing SPRITE results using ChimeraX. However, I am facing an issue with the syntax for aligning the residues of *2HNT* with *1A0J*. The module I am using, which was provided by Basil (attached with this email), includes syntax for Chimera (refer to Figures 10 and 11 in the attached document). I have tried adapting the syntax for ChimeraX but have not been successful. I would really appreciate your guidance on this matter or if you could direct me to someone who might be able to assist in generating the correct command line syntax. Thank you so much for your time and help! Zeenat -- *Dr. Zeenat Bashir* *Senior Lecturer* *Biotechnology Lab Coordinator* *Department of Chemical and Biomolecular Engineering* *University of Pennsylvania* *310 Towne Building* *220 S. 33rd Street* *Philadelphia, 19104 -6393* bashirz(a)seas.upenn.edu

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Roll command for multi objects in grid
by Enrico Martinez 18 Feb '25

18 Feb '25

Dear ChimeraX users! Using til command I split six superimposed structures, displaying them as the 2x3 table and then rotate each object along its axis within each grid using "roll" in the following way: # for 6 different object roll models #1 center #1 & protein roll models #2 center #2 & protein roll models #3 center #3 & protein roll models #4 center #4 & protein roll models #5 center #5 & protein roll models #6 center #6 & protein Would it be possible to simplify this to one "roll" command that will automatically rotate all displayed objects in the separate grids along its axis ? Many thanks in advance Enrico

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Questions about match and view commands
by Enrico Martinez 16 Feb '25

16 Feb '25

Dear ChimeraX users! I am performing a visualization of the ensemble of conformers for the same protein defined in the chimerax as models #1 to #6. Here are some of my questions: 1 - I try to superimpose all structures to the first model using match #2-5 to #1 is it possible to use some regular expression instead of #2-5 to select all models from the second to the last e.g. to superimpose all structures to the first one in the script. 2 - I try to automatically orient the superimposed models along its principal axe in one command e.g. using view orient but it does not produce a proper orientation. What kind of trick could work for a nanobody object to orient it automatically e,g, along Z ? Many thanks in advance Enrico

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assistance on bundle writting
by Nguyen, Catherine 14 Feb '25

14 Feb '25

Hello, I was hoping to get your help. I am trying to write a bundle and I am struggling to figure out how I can add psuedo-bonds using python as I want to connect two amino acids by the CA. Would you be able to help me find a way to do this? I hope to hear from you soon, Best wishes, Catherine

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MUNKI Managed Software Download URL
by Antony Nelson 14 Feb '25

14 Feb '25

Hi, I appreciate this might seem an odd request, but do you have a public download location for ChimeraX software? There exists a widely used system by which administrators of Apple computers distribute software to their users by means of applications known as Munki and Autopkgr. Software which can be downloaded from public websites can be managed in such a way that new releases and updates are automatically added to the software repository Apple administrators curate for their users. Without making this publicly available, admins will only update your software when users request the admins to do so. Looking back on the Loupe Browser instances that have been made available to my users, they have only had access to versions: 0.8.0 0.9.0 0.9.1 0.93.0 1.1.1 1.7.1 and today they will have 1.9.0 If your software was made available via public download by a predictable URL, then they would have had access to every version released on the day it was added to your website since it was first requested by users. If you are concerned about the acceptance of terms of conditions then perhaps this could be incorporated into the URL string. Regards

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How to get different silhouette widths for 2 maps
by Hong ZHAN 13 Feb '25

13 Feb '25

Hi there, I am trying to create a video with two maps overlay with different silhouette widths. It is easy to do with 2 images, but how I can do it in a video setting? If I change the width to 6, all maps changes the width to 6. Thanks! -Hong

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Unable to load scripts at startup
by Pranav Shah 13 Feb '25

13 Feb '25

Hi Team, (I accidentally sent this to ChimeraX-bugs, copying it again here) I am trying to load some scripts at startup via the chimerax_custom_functions.cxc command file - open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc in the log file I see the following message: still retrieving bundle list from toolshed open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py Error running startup command 'open /Users/ps/.chimerax/chimerax_commands/chimerax_custom_functions.cxc': Unknown command: open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py This is strange as simply running "open /Users/ps/.chimerax/chimerax_commands/chimerax_molmap_cube.py" in the ChimeraX command panel runs perfectly fine! the error occurs only when I try to run that line through the .cxc file. Am I missing something? or could this be a bug? I am on the stable release of ChimeraX (version 1.9). Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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PAEcontacts colorkey
by ccinsua＠gmail.com 13 Feb '25

13 Feb '25

Hi all, Thank you very much for your work with chimerax. I've been using it to study alphafold complex prediction, and I find the command alphafold contacts very useful. The default color key (guess it is paecontacts, according to documentation) ranges are blue (low PAE) - green (medium PAE) - yellow (high PAE). However, I am unable to add a color key using "key paecontacts". Somehow I have to define it myself. Is there anything I am missing? I would like to stick to the blue-green-yellow scheme. Thanks a lot in advance Carlos

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NASA - Country of Origin Statement and 508 Conformance Request: UCSF ChimeraX
by Price, Dru C. (LARC-B730)[eMITS] 12 Feb '25

12 Feb '25

Hello, my name is Dru and I work for the NASA Commercial IT Acquisition Team. As such, I ensure that all NASA acquisitions of Covered Articles comply with Title II; General Provision Section 208 and Title V; General Provisions Section 514 of the Consolidated Appropriations Act, 2021, Public Law 116-260<https://www.congress.gov/bill/116th-congress/house-bill/133/text>, enacted December 27, 2020. To do so, the Country of Origin (CoO) information must be obtained from the company that develops, produces, manufactures, or assembles the product(s). Please specifically identify the country, or countries, in which each of the following software products is developed and maintained: * UCSF ChimeraX Additionally, if available, please identify all authorized resellers of the product(s) in question. Finally, I am requesting an Accessibility Conformance Report (starting from Page 10 of the attached VPAT) be completed and returned so that NASA can assess the product's level of 508 Conformance. More information regarding Section 508 of the Rehabilitation Act of 1973 and what it means to manufacturers/developers can be found at https://www.section508.gov/sell/vpat. I have attached a blank copy of the latest revision of the VPAT standard if you do not already have a completed VPAT available for this product. Please complete this document to the best of your abilities, if one is not already available. Product / Service Description Model Number Country of Origin Is final testing performed in the United States? Please let me know if you have any questions. Thank you, Dru C. Price Procurement Analyst eMITS | [ROTHE ARES JV] Commercial IT Management Support Croscutting Agency Service (CAS) Branch Enterprise Business Management Office (EBMO) NASA - Office of the Chief Information Office (OCIO) [cid:image001.png@01DB7D5D.40BD4D20]<https://teams.microsoft.com/l/chat/0/0?users=dru.c.price@nasa.gov> [cid:image002.png@01DB7D5D.40BD4D20]

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